Non-coding Transcription Instructs Chromatin Folding and Compartmentalization to Dictate Enhancer-Promoter Communication and T Cell Fate

[1]  William J R Longabaugh,et al.  Bcl11b and combinatorial resolution of cell fate in the T-cell gene regulatory network , 2017, Proceedings of the National Academy of Sciences.

[2]  Bas van Steensel,et al.  Lamina-Associated Domains: Links with Chromosome Architecture, Heterochromatin, and Gene Repression , 2017, Cell.

[3]  S. Ogawa,et al.  The E‐Id Protein Axis Specifies Adaptive Lymphoid Cell Identity and Suppresses Thymic Innate Lymphoid Cell Development , 2017, Immunity.

[4]  Niels Galjart,et al.  Cohesin is positioned in mammalian genomes by transcription, CTCF and Wapl , 2017, Nature.

[5]  R. Young,et al.  A Phase Separation Model for Transcriptional Control , 2017, Cell.

[6]  Harri Lähdesmäki,et al.  TET proteins regulate the lineage specification and TCR-mediated expansion of iNKT cells , 2016, Nature Immunology.

[7]  E. Lander,et al.  Local regulation of gene expression by lncRNA promoters, transcription and splicing , 2016, Nature.

[8]  Hao Yuan Kueh,et al.  Asynchronous combinatorial action of four regulatory factors activates Bcl11b for T cell commitment , 2016, Nature Immunology.

[9]  J. Rinn,et al.  "Cat's Cradling" the 3D Genome by the Act of LncRNA Transcription. , 2016, Molecular cell.

[10]  L. Mirny,et al.  Formation of Chromosomal Domains in Interphase by Loop Extrusion , 2015, bioRxiv.

[11]  M. Gullerová,et al.  Transcription facilitates sister chromatid cohesion on chromosomal arms , 2016, Nucleic acids research.

[12]  E. Rothenberg,et al.  Forging T-Lymphocyte Identity: Intersecting Networks of Transcriptional Control. , 2016, Advances in immunology.

[13]  Neva C. Durand,et al.  Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes , 2015, Proceedings of the National Academy of Sciences.

[14]  C. Benner,et al.  New roles for DNA cytosine modification, eRNA, anchors, and superanchors in developing B cell progenitors , 2015, Proceedings of the National Academy of Sciences.

[15]  Siddharth S. Dey,et al.  Genome-wide Maps of Nuclear Lamina Interactions in Single Human Cells , 2015, Cell.

[16]  Aaron N. Chang,et al.  Brg1 activates enhancer repertoires to establish B cell identity and modulate cell growth , 2015, Nature Immunology.

[17]  Zhe Zhang,et al.  Germline Gain-of-Function Mutations in AFF4 Cause a Developmental Syndrome Functionally Linking the Super Elongation Complex and Cohesin , 2015, Nature Genetics.

[18]  M. Levine,et al.  Regulatory Principles Governing Tissue Specificity of Developmental Enhancers. , 2015, Cold Spring Harbor symposia on quantitative biology.

[19]  Neva C. Durand,et al.  A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping , 2014, Cell.

[20]  R. Young,et al.  An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element , 2014, Science.

[21]  Ellen V. Rothenberg,et al.  Developmental gene networks: a triathlon on the course to T cell identity , 2014, Nature Reviews Immunology.

[22]  Yaojun Zhang,et al.  3D Trajectories Adopted by Coding and Regulatory DNA Elements: First-Passage Times for Genomic Interactions , 2014, Cell.

[23]  L. Klein,et al.  Positive and negative selection of the T cell repertoire: what thymocytes see (and don't see) , 2014, Nature Reviews Immunology.

[24]  C. Murre,et al.  The establishment of B versus T cell identity. , 2014, Trends in immunology.

[25]  Michael Q. Zhang,et al.  BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data , 2013, BMC Genomics.

[26]  Howard Y. Chang,et al.  Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position , 2013, Nature Methods.

[27]  H. Kueh,et al.  A far downstream enhancer for murine Bcl11b controls its T-cell specific expression. , 2013, Blood.

[28]  R. Jaenisch,et al.  One-Step Generation of Mice Carrying Reporter and Conditional Alleles by CRISPR/Cas-Mediated Genome Engineering , 2013, Cell.

[29]  A. Cumano,et al.  GATA-3 promotes T-cell specification by repressing B-cell potential in pro-T cells in mice. , 2013, Blood.

[30]  P. Ferrier Faculty Opinions recommendation of Global changes in the nuclear positioning of genes and intra- and interdomain genomic interactions that orchestrate B cell fate. , 2012 .

[31]  C. Glass,et al.  Positive intergenic feedback circuitry, involving EBF1 and FOXO1, orchestrates B-cell fate , 2012, Proceedings of the National Academy of Sciences.

[32]  B. Williams,et al.  Dynamic Transformations of Genome-wide Epigenetic Marking and Transcriptional Control Establish T Cell Identity , 2012, Cell.

[33]  J. Downing,et al.  The BCL11B tumor suppressor is mutated across the major molecular subtypes of T-cell acute lymphoblastic leukemia. , 2011, Blood.

[34]  Alejandro Chavez,et al.  A critical role for TCF-1 in T-lineage specification and differentiation , 2011, Nature.

[35]  Shannon Burke,et al.  Critical roles of Bcl11b in T‐cell development and maintenance of T‐cell identity , 2010, Immunological reviews.

[36]  R. Kominami,et al.  An Essential Developmental Checkpoint for Production of the T Cell Lineage , 2010, Science.

[37]  Lia S. Campos,et al.  Reprogramming of T Cells to Natural Killer–Like Cells upon Bcl11b Deletion , 2010, Science.

[38]  M. Leid,et al.  An Early T Cell Lineage Commitment Checkpoint Dependent on the Transcription Factor Bcl11b , 2010, Science.

[39]  C. Glass,et al.  Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. , 2010, Molecular cell.

[40]  Lee E. Edsall,et al.  Human DNA methylomes at base resolution show widespread epigenomic differences , 2009, Nature.

[41]  I. Amit,et al.  Comprehensive mapping of long range interactions reveals folding principles of the human genome , 2011 .

[42]  Lior Pachter,et al.  Sequence Analysis , 2020, Definitions.

[43]  N. Speck,et al.  Core binding factors are necessary for natural killer cell development and cooperate with Notch signaling during T-cell specification. , 2008, Blood.

[44]  R. Kominami,et al.  Haploinsufficiency of Bcl11b for suppression of lymphomagenesis and thymocyte development. , 2007, Biochemical and biophysical research communications.

[45]  Hiroshi Kawamoto,et al.  E proteins and Notch signaling cooperate to promote T cell lineage specification and commitment , 2006, The Journal of experimental medicine.

[46]  R. Paro,et al.  Intergenic transcription through a polycomb group response element counteracts silencing. , 2005, Genes & development.

[47]  Andrew P. Weng,et al.  Activating Mutations of NOTCH1 in Human T Cell Acute Lymphoblastic Leukemia , 2004, Science.

[48]  Thomas M. Schmitt,et al.  Induction of T cell development from hematopoietic progenitor cells by delta-like-1 in vitro. , 2002, Immunity.

[49]  K. Nasmyth THE GENOME : Joining , Resolving , and Separating Sister Chromatids During Mitosis and Meiosis , 2006 .

[50]  B. Osborne Transcriptional control of T cell development. , 2000, Current opinion in immunology.

[51]  M. Carleton,et al.  Signals transduced by CD3epsilon, but not by surface pre-TCR complexes, are able to induce maturation of an early thymic lymphoma in vitro. , 1999, Journal of immunology.

[52]  C. Murre,et al.  The role of E-proteins in B- and T-lymphocyte development. , 1998, Seminars in immunology.